Hello,

I hope this email finds you well. My name is Louis OIiveira, and I am a Master's student specializing in protein crystallography at the University of São Paulo.

I am currently using Chimera X for generating images of the structure I am studying. However, I have encountered some issues that I am struggling to resolve. Specifically, I have successfully validated the structure of the enzyme and am now attempting to present the co-crystallized ligand along with its electronic density map interacting with the enzyme.

My challenge lies in isolating the electronic density of the ligand without including the electronic density of the nearby residues. I have attempted to use the "zone" function in the map menu, but I am still seeing some electronic density that I wish to exclude as shown in the picture .

I would greatly appreciate your guidance on how to effectively isolate the electronic density of the ligand in Chimera X. If you have any insights or recommendations, I would be grateful for your assistance.

Thank you for your time, and I look forward to hearing from you soon.

Best regards,

Louis Oliveira Master's Student Instituto de Fisica de São Carlos University of São Paulo